RchiOBHm_Chr5g0049101

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0000370
Physical Location & Seq
Forward (+)
46526590 .. 46533672
7083 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ32678

Sequence Viewer

Length: 951 bp
ATGGATCCTCAGAGATGCAGGGCCAAGGTTAGCGGCATGATTACCTCTCAAGAGGAGTTCTATCTTGAGAAGGAGGTGGTGCAACCTGTTCCATCTATTGTTGGGATGGTTGATGCTACTCACCTAACTAGGCTGACTAGGGAAGTCATTAGATTGGGGGCAGTGGCATTTCAGGGTGGTACAGATTACTTGTTGGCTAATCAGTGGATTGAGAACATGGAGACCTACTATGATATGGTTGTCTGTACTGACATGGAGAAGAAGATTACAGCTACGTTCCTTCTCCAGGGTGAGGCGGGACAGTGGTGGGATTCTATGCTGAAGACAAGGAACATATCGACCATTACTTGGGAGGGTTTTGTGGAACTCTTTCGGGACATGTACCTTCCCGCTTCTAGGAGGGAGAAATTGGGGGTTGACTTCATTTCTCTAGTCCAGGGGACTATGAGTGTCAAGGGCTATGAGGCCCGATTCTCACAATTGTACCGGTTTGTTAGGCCGATGGATCCAGTGTCTTTGGCTCGGAAGTTCCAACGGGGACTGAATCTGGTGATCAGAGATAGGGTGACTCCTTTTCAGTTGCCTACTGTGGCACTTATCTTTGCTAGTGCTCTTAGATTTGAGCAAGAACTTCTAACGTCTCGAGGGGAGATGACTACTATGGGAGATTCCCAGGGAAAGGGAAAGGCAGTTGCCGGGAGCAGTGATGAGATGGACAGTCAGGGTGGATCCTGGAAGAGACAGCGGACTTATCATAAGGCGCCTGCTAGGGTAGCAGCTGCACTTGTTGGGCAGGCAGCACACCTGAGATGTTACAACTGCGGCGAGTTAGACCATGTTTCCAAAGTGTGCACGAAGCCGAGGAGCAAGGTATGCTTTAGATGTGGCCAGACTGGGCATGTAGCCAGAGAGTGTACTCGACCTCAAGATGGCAGGCAGGGGAACCAATAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RVP_2 Retrotrans_gag zf-CCHC

Protein Analysis

316

Amino Acids

35.66

Weight (kDa)

9.08

Isoelectric Point (pI)

39.62

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 55 - 182 1.3e-06 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 91 - 182 5.2e-18 Retrotransposon gag protein
zf-CCHC PF00098 291 - 306 3.7e-07 Zinc knuckle
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 760
AccB7I CCANNNNNTGG 1 cut(s) 348
AciI CCGC 5 cut(s) 33, 296, 390, 745, 822
AclWI GGATC 5 cut(s) 12, 500, 513, 723, 736
AcoI YGGCCR 1 cut(s) 886
AcuI CTGAAG 1 cut(s) 341
AcyI GRCGYC 1 cut(s) 761
AfaI GTAC 5 cut(s) 181, 247, 383, 485, 916
AfiI CCNNNNNNNGG 6 cut(s) 286, 292, 348, 396, 679, 929
AflIII ACRYGT 1 cut(s) 378
AgeI ACCGGT 1 cut(s) 486
AjnI CCWGG 4 cut(s) 285, 435, 672, 731
AluBI AGCT 2 cut(s) 272, 779
AluI AGCT 2 cut(s) 272, 779
Alw21I GWGCWC 2 cut(s) 613, 854
Alw26I GTCTC 3 cut(s) 215, 645, 733
Alw44I GTGCAC 1 cut(s) 850
AlwI GGATC 5 cut(s) 12, 500, 513, 723, 736
Ama87I CYCGRG 1 cut(s) 642
AoxI GGCC 4 cut(s) 21, 465, 497, 886
ApaLI GTGCAC 1 cut(s) 850
ApeKI GCWGC 3 cut(s) 776, 779, 797
AsiGI ACCGGT 1 cut(s) 486
Asp700I GAANNNNTTC 1 cut(s) 369
AspLEI GCGC 1 cut(s) 763
AspS9I GGNCC 2 cut(s) 21, 466
AsuC2I CCSGG 1 cut(s) 697
AsuHPI GGTGA 4 cut(s) 113, 302, 562, 577
AvaI CYCGRG 1 cut(s) 642
BaeGI GKGCMC 1 cut(s) 854
BaeI ACNNNNGTAYC 2 cut(s) 467, 500
BalI TGGCCA 1 cut(s) 888
BamHI GGATCC 3 cut(s) 4, 505, 728
BanI GGYRCC 1 cut(s) 760
BbsI GAAGAC 1 cut(s) 329
Bbv12I GWGCWC 2 cut(s) 613, 854
BbvI GCAGC 3 cut(s) 766, 788, 809
BccI CCATC 5 cut(s) 100, 100, 496, 706, 923
BciT130I CCWGG 4 cut(s) 287, 437, 674, 733
BclI TGATCA 1 cut(s) 552
BcnI CCSGG 1 cut(s) 697
BcoDI GTCTC 3 cut(s) 215, 645, 733
BfaI CTAG 6 cut(s) 129, 138, 396, 431, 606, 768
BfoI RGCGCY 1 cut(s) 764
BisI GCNGC 5 cut(s) 34, 777, 780, 798, 823
BlsI GCNGC 5 cut(s) 35, 778, 781, 799, 824
Bme1390I CCNGG 5 cut(s) 287, 437, 674, 697, 733
BmeT110I CYCGRG 1 cut(s) 642
BmgT120I GGNCC 2 cut(s) 21, 466
BmiI GGNNCC 5 cut(s) 6, 507, 730, 762, 944
BmrFI CCNGG 5 cut(s) 287, 437, 674, 697, 733
BmrI ACTGGG 1 cut(s) 903
BmsI GCATC 2 cut(s) 5, 103
BmuI ACTGGG 1 cut(s) 903
BpiI GAAGAC 1 cut(s) 329
BpmI CTGGAG 1 cut(s) 269
BpuEI CTTGAG 3 cut(s) 33, 86, 909
BpuMI CCSGG 1 cut(s) 697
BsaHI GRCGYC 1 cut(s) 761
BsaI GGTCTC 1 cut(s) 215
BsaJI CCNNGG 6 cut(s) 24, 286, 436, 672, 673, 860
BsaWI WCCGGW 1 cut(s) 486
Bsc4I CCNNNNNNNGG 6 cut(s) 286, 292, 348, 396, 679, 929
Bse118I RCCGGY 1 cut(s) 486
Bse1I ACTGG 2 cut(s) 509, 898
BseBI CCWGG 4 cut(s) 287, 437, 674, 733
BseDI CCNNGG 6 cut(s) 24, 286, 436, 672, 673, 860
BseGI GGATG 1 cut(s) 111
BseLI CCNNNNNNNGG 6 cut(s) 286, 292, 348, 396, 679, 929
BseMII CTCAG 2 cut(s) 23, 797
BseNI ACTGG 2 cut(s) 509, 898
BseRI GAGGAG 2 cut(s) 68, 877
BseSI GKGCMC 1 cut(s) 854
BseXI GCAGC 3 cut(s) 766, 788, 809
BsgI GTGCAG 1 cut(s) 765
BshFI GGCC 4 cut(s) 23, 467, 499, 888
BshNI GGYRCC 1 cut(s) 760
BshTI ACCGGT 1 cut(s) 486
BsiHKAI GWGCWC 2 cut(s) 613, 854
BsiHKCI CYCGRG 1 cut(s) 642
BsiSI CCGG 2 cut(s) 487, 696
BslFI GGGAC 4 cut(s) 312, 389, 454, 552
BslI CCNNNNNNNGG 6 cut(s) 286, 292, 348, 396, 679, 929
BsmAI GTCTC 3 cut(s) 215, 645, 733
BsmBI CGTCTC 1 cut(s) 645
BsmFI GGGAC 4 cut(s) 312, 389, 454, 552
BsnI GGCC 4 cut(s) 23, 467, 499, 888
Bso31I GGTCTC 1 cut(s) 215
BsoBI CYCGRG 1 cut(s) 642
Bsp1286I GDGCHC 2 cut(s) 613, 854
Bsp143I GATC 4 cut(s) 4, 505, 552, 728
BspACI CCGC 5 cut(s) 33, 296, 390, 745, 822
BspANI GGCC 4 cut(s) 23, 467, 499, 888
BspCNI CTCAG 2 cut(s) 22, 798
BspLI GGNNCC 5 cut(s) 6, 507, 730, 762, 944
BspPI GGATC 5 cut(s) 12, 500, 513, 723, 736
BspT107I GGYRCC 1 cut(s) 760
BspTNI GGTCTC 1 cut(s) 215
BsrFI RCCGGY 1 cut(s) 486
BsrI ACTGG 2 cut(s) 509, 898
BssAI RCCGGY 1 cut(s) 486
BssECI CCNNGG 6 cut(s) 24, 286, 436, 672, 673, 860
BssMI GATC 4 cut(s) 4, 505, 552, 728
BssNI GRCGYC 1 cut(s) 761
BssT1I CCWWGG 1 cut(s) 24
Bst2UI CCWGG 4 cut(s) 287, 437, 674, 733
Bst4CI ACNGT 3 cut(s) 303, 589, 719
Bst6I CTCTTC 1 cut(s) 731
BstACI GRCGYC 1 cut(s) 761
BstAPI GCANNNNNTGC 1 cut(s) 873
BstC8I GCNNGC 3 cut(s) 765, 795, 935
BstDEI CTNAG 3 cut(s) 9, 614, 806
BstENI CCTNNNNNAGG 1 cut(s) 284
BstF5I GGATG 1 cut(s) 111
BstH2I RGCGCY 1 cut(s) 764
BstHHI GCGC 1 cut(s) 763
BstKTI GATC 4 cut(s) 7, 508, 555, 731
BstMAI GTCTC 3 cut(s) 215, 645, 733
BstMBI GATC 4 cut(s) 4, 505, 552, 728
BstMWI GCNNNNNNNGC 2 cut(s) 773, 873
BstNI CCWGG 4 cut(s) 287, 437, 674, 733
BstNSI RCATGY 2 cut(s) 382, 902
BstSCI CCNGG 5 cut(s) 285, 435, 672, 695, 731
BstSLI GKGCMC 1 cut(s) 854
BstV1I GCAGC 3 cut(s) 766, 788, 809
BstV2I GAAGAC 1 cut(s) 329
BstX2I RGATCY 3 cut(s) 4, 505, 728
BstYI RGATCY 3 cut(s) 4, 505, 728
BsuRI GGCC 4 cut(s) 23, 467, 499, 888
BtsCI GGATG 1 cut(s) 111
BtsI GCAGTG 2 cut(s) 168, 709
BtsIMutI CAGTG 5 cut(s) 168, 209, 308, 516, 709
Cac8I GCNNGC 3 cut(s) 765, 795, 935
CfoI GCGC 1 cut(s) 763
Cfr10I RCCGGY 1 cut(s) 486
Cfr13I GGNCC 2 cut(s) 21, 466
Csp6I GTAC 5 cut(s) 180, 246, 382, 484, 915
CspAI ACCGGT 1 cut(s) 486
CviAII CATG 6 cut(s) 37, 217, 253, 379, 836, 899
CviQI GTAC 5 cut(s) 180, 246, 382, 484, 915
DdeI CTNAG 3 cut(s) 9, 614, 806
DinI GGCGCC 1 cut(s) 762
DpnI GATC 4 cut(s) 6, 507, 554, 730
DpnII GATC 4 cut(s) 4, 505, 552, 728
EaeI YGGCCR 1 cut(s) 886
Eam1104I CTCTTC 1 cut(s) 731
EarI CTCTTC 1 cut(s) 731
Eco130I CCWWGG 1 cut(s) 24
Eco31I GGTCTC 1 cut(s) 215
Eco57I CTGAAG 1 cut(s) 341
Eco88I CYCGRG 1 cut(s) 642
EcoNI CCTNNNNNAGG 1 cut(s) 284
EcoRII CCWGG 4 cut(s) 285, 435, 672, 731
EcoT14I CCWWGG 1 cut(s) 24
EgeI GGCGCC 1 cut(s) 762
EheI GGCGCC 1 cut(s) 762
ErhI CCWWGG 1 cut(s) 24
Esp3I CGTCTC 1 cut(s) 645
FaeI CATG 6 cut(s) 40, 220, 256, 382, 839, 902
FalI AAGNNNNNCTT 2 cut(s) 860, 892
FaqI GGGAC 4 cut(s) 312, 389, 454, 552
FatI CATG 6 cut(s) 36, 216, 252, 378, 835, 898
FauI CCCGC 2 cut(s) 289, 397
FbaI TGATCA 1 cut(s) 552
Fnu4HI GCNGC 5 cut(s) 34, 777, 780, 798, 823
FokI GGATG 1 cut(s) 118
Fsp4HI GCNGC 5 cut(s) 34, 777, 780, 798, 823
FspBI CTAG 6 cut(s) 129, 138, 396, 431, 606, 768
GlaI GCGC 1 cut(s) 762
GluI GCNGC 5 cut(s) 34, 777, 780, 798, 823
GsuI CTGGAG 1 cut(s) 269
HaeII RGCGCY 1 cut(s) 764
HaeIII GGCC 4 cut(s) 23, 467, 499, 888
HapII CCGG 2 cut(s) 487, 696
HhaI GCGC 1 cut(s) 763
Hin1I GRCGYC 1 cut(s) 761
Hin1II CATG 6 cut(s) 40, 220, 256, 382, 839, 902
Hin6I GCGC 1 cut(s) 761
HinP1I GCGC 1 cut(s) 761
HincII GTYRAC 1 cut(s) 418
HindII GTYRAC 1 cut(s) 418
HinfI GANTC 5 cut(s) 311, 471, 544, 568, 668
HpaII CCGG 2 cut(s) 487, 696
HphI GGTGA 4 cut(s) 113, 302, 562, 577
Hpy166II GTNNAC 3 cut(s) 418, 852, 915
Hpy188I TCNGA 3 cut(s) 12, 525, 557
Hpy188III TCNNGA 5 cut(s) 50, 65, 374, 642, 926
Hpy8I GTNNAC 3 cut(s) 418, 852, 915
HpyAV CCTTC 3 cut(s) 64, 290, 395
HpyCH4III ACNGT 3 cut(s) 303, 589, 719
HpyCH4IV ACGT 2 cut(s) 275, 638
HpyCH4V TGCA 4 cut(s) 18, 82, 782, 852
HpyF10VI GCNNNNNNNGC 2 cut(s) 773, 873
HpyF3I CTNAG 3 cut(s) 9, 614, 806
HpySE526I ACGT 2 cut(s) 275, 638
Hsp92I GRCGYC 1 cut(s) 761
Hsp92II CATG 6 cut(s) 40, 220, 256, 382, 839, 902
HspAI GCGC 1 cut(s) 761
KasI GGCGCC 1 cut(s) 760
Ksp22I TGATCA 1 cut(s) 552
Kzo9I GATC 4 cut(s) 4, 505, 552, 728
LmnI GCTCC 2 cut(s) 699, 864
Lsp1109I GCAGC 3 cut(s) 766, 788, 809
LweI GCATC 2 cut(s) 5, 103
MaeI CTAG 6 cut(s) 129, 138, 396, 431, 606, 768
MaeII ACGT 2 cut(s) 275, 638
MaeIII GTNAC 2 cut(s) 565, 812
MalI GATC 4 cut(s) 6, 507, 554, 730
MboI GATC 4 cut(s) 4, 505, 552, 728
MboII GAAGA 4 cut(s) 271, 274, 334, 748
MfeI CAATTG 1 cut(s) 479
MflI RGATCY 3 cut(s) 4, 505, 728
MhlI GDGCHC 2 cut(s) 613, 854
MlsI TGGCCA 1 cut(s) 888
MluCI AATT 2 cut(s) 407, 479
MluNI TGGCCA 1 cut(s) 888
Mly113I GGCGCC 1 cut(s) 761
MlyI GAGTC 1 cut(s) 562
MmeI TCCRAC 1 cut(s) 556
Mox20I TGGCCA 1 cut(s) 888
MroXI GAANNNNTTC 1 cut(s) 369
MscI TGGCCA 1 cut(s) 888
Msp20I TGGCCA 1 cut(s) 888
MspA1I CMGCKG 2 cut(s) 745, 779
MspI CCGG 2 cut(s) 487, 696
MspR9I CCNGG 5 cut(s) 287, 437, 674, 697, 733
MunI CAATTG 1 cut(s) 479
MvaI CCWGG 4 cut(s) 287, 437, 674, 733
MwoI GCNNNNNNNGC 2 cut(s) 773, 873
NarI GGCGCC 1 cut(s) 761
NciI CCSGG 1 cut(s) 697
NdeII GATC 4 cut(s) 4, 505, 552, 728
NlaIII CATG 6 cut(s) 40, 220, 256, 382, 839, 902
NlaIV GGNNCC 5 cut(s) 6, 507, 730, 762, 944
NmeAIII GCCGAG 1 cut(s) 885
NmuCI GTSAC 1 cut(s) 565
NspI RCATGY 2 cut(s) 382, 902
PaeR7I CTCGAG 1 cut(s) 642
PasI CCCWGGG 1 cut(s) 673
PciI ACATGT 1 cut(s) 378
PdmI GAANNNNTTC 1 cut(s) 369
PfeI GAWTC 4 cut(s) 311, 471, 544, 668
PflMI CCANNNNNTGG 1 cut(s) 348
PfoI TCCNGGA 1 cut(s) 731
PinAI ACCGGT 1 cut(s) 486
PkrI GCNGC 5 cut(s) 35, 778, 781, 799, 824
PleI GAGTC 1 cut(s) 562
PluTI GGCGCC 1 cut(s) 764
PpsI GAGTC 1 cut(s) 562
PscI ACATGT 1 cut(s) 378
Psp6I CCWGG 4 cut(s) 285, 435, 672, 731
PspGI CCWGG 4 cut(s) 285, 435, 672, 731
PspN4I GGNNCC 5 cut(s) 6, 507, 730, 762, 944
PspPI GGNCC 2 cut(s) 21, 466
PsuI RGATCY 3 cut(s) 4, 505, 728
PvuII CAGCTG 1 cut(s) 779
RsaI GTAC 5 cut(s) 181, 247, 383, 485, 916
RsaNI GTAC 5 cut(s) 180, 246, 382, 484, 915
SatI GCNGC 5 cut(s) 34, 777, 780, 798, 823
Sau3AI GATC 4 cut(s) 4, 505, 552, 728
Sau96I GGNCC 2 cut(s) 21, 466
SchI GAGTC 1 cut(s) 562
ScrFI CCNGG 5 cut(s) 287, 437, 674, 697, 733
SduI GDGCHC 2 cut(s) 613, 854
SfaNI GCATC 2 cut(s) 5, 103
SfoI GGCGCC 1 cut(s) 762
Sfr274I CTCGAG 1 cut(s) 642
SlaI CTCGAG 1 cut(s) 642
SmlI CTYRAG 4 cut(s) 48, 65, 642, 924
SmoI CTYRAG 4 cut(s) 48, 65, 642, 924
Sse9I AATT 2 cut(s) 407, 479
SsiI CCGC 5 cut(s) 33, 296, 390, 745, 822
SspDI GGCGCC 1 cut(s) 760
SspMI CTAG 6 cut(s) 129, 138, 396, 431, 606, 768
StyD4I CCNGG 5 cut(s) 285, 435, 672, 695, 731
StyI CCWWGG 1 cut(s) 24
TaaI ACNGT 3 cut(s) 303, 589, 719
TaiI ACGT 2 cut(s) 278, 641
TaqI TCGA 3 cut(s) 338, 643, 919
TasI AATT 2 cut(s) 407, 479
TatI WGTACW 2 cut(s) 245, 914
TauI GCSGC 2 cut(s) 36, 825
TfiI GAWTC 4 cut(s) 311, 471, 544, 668
TscAI CASTG 5 cut(s) 168, 209, 308, 516, 709
TseFI GTSAC 1 cut(s) 565
TseI GCWGC 3 cut(s) 776, 779, 797
Tsp45I GTSAC 1 cut(s) 565
TspDTI ATGAA 1 cut(s) 412
TspRI CASTG 5 cut(s) 168, 209, 308, 516, 709
Van91I CCANNNNNTGG 1 cut(s) 348
VneI GTGCAC 1 cut(s) 850
XagI CCTNNNNNAGG 1 cut(s) 284
XceI RCATGY 2 cut(s) 382, 902
XhoI CTCGAG 1 cut(s) 642
XmnI GAANNNNTTC 1 cut(s) 369
XspI CTAG 6 cut(s) 129, 138, 396, 431, 606, 768
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.